- PDB-5b34: Serial Femtosecond Crystallography (SFX) of Ground State Bacterio... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5b34
Title
Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with Iodine-labeled Detergent HAD13a Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA
Components
Bacteriorhodopsin
Keywords
PROTON TRANSPORT / Membrane protein / Proton pump / Transport Protein / Retinal / SAD
Function / homology
Function and homology information
light-driven active monoatomic ion transmembrane transporter activity / photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
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Details
Nonpolymer details
4QL A 302 (303) and OCT A 304 (305) place the alternate positions.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal grow
Temperature: 293 K / Method: batch mode Details: 25%(w/v) DMPC/CHAPSO bicelles, 3.2 M NaH2PO4, 3.5%(w/v) triethylene glycol, 180 mM 1,6-hexanediol, 4 mM HAD13a
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Data collection
Diffraction
Mean temperature: 293 K
Diffraction source
Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.771 Å
Detector
Type: MPCCD / Detector: CCD / Date: Nov 22, 2015
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.771 Å / Relative weight: 1
Reflection
Resolution: 2.1→50 Å / Num. obs: 18388 / % possible obs: 100 % / Redundancy: 107.6 % / Net I/σ(I): 5.7
Reflection shell
Resolution: 2.1→2.17 Å
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0131
refinement
Cheetah
dataextraction
CrystFEL
dataprocessing
SHELX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.701 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.156 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21604
882
4.8 %
RANDOM
Rwork
0.16339
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obs
0.16601
17471
99.96 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å